Jason P. Gleghorn

Logan Halle, Jason P. Gleghorn

Bidirectional transformers are the foundation of many sequence modeling tasks across natural, biological, and chemical language domains, but they are permutation-invariant without explicit positional embeddings. In contrast, unidirectional attention inherently encodes positional information through its triangular mask, enabling models to operate without positional embeddings altogether. Here, we introduce Dual Triangle Attention, a novel bidirectional attention mechanism that separates the query-key subspace of each attention head into two complementary triangular masks: one that attends to past-and-self positions and one that attends to future-and-self positions. This design provides bidirectional context while maintaining the causal mask's implicit positional inductive bias in both directions. Using PyTorch's flex_attention, Dual Triangle Attention is implemented as a single compiled kernel call with no additional parameters beyond standard multi-head attention. We evaluated Dual Triangle Attention across three settings: (1) a synthetic argmax position probe, (2) masked language modeling (MLM) on natural language, and (3) MLM on protein sequences. In the argmax task, both Dual Triangle Attention and causal attention learn positional information without explicit positional embeddings, whereas standard bidirectional attention cannot. In the MLM experiments, Dual Triangle Attention with Rotary Positional Embeddings (RoPE) achieved the best context extension performance and strong performance across the board. These findings suggest that Dual Triangle Attention is a viable attention mechanism for bidirectional transformers, with or without positional embeddings.

Logan Hallee, Rohan Kapur, Arjun Patel et al.

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, but they still struggle with highly discriminative tasks and may produce sub-optimal representations of important documents like scientific literature. With the increased reliance on retrieval augmentation and search, representing diverse documents as concise and descriptive vectors is crucial. This paper improves upon the vectors embeddings of scientific text by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We apply a novel Mixture of Experts (MoE) extension pipeline to pretrained BERT models, where every multi-layer perceptron section is enlarged and copied into multiple distinct experts. Our MoE variants perform well over $N$ scientific domains with $N$ dedicated experts, whereas standard BERT models excel in only one domain at a time. Notably, extending just a single transformer block to MoE captures 85% of the benefit seen from full MoE extension at every layer. This holds promise for versatile and efficient One-Size-Fits-All transformer networks for numerically representing diverse inputs. Our methodology marks advancements in representation learning and holds promise for enhancing vector database search and compilation.